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jhourani edited this page Jul 13, 2012 · 42 revisions

KAM Navigator Cytoscape Plugin User Manual

KAM Navigator is a Cytoscape plugin that allows users of the OpenBEL Framework to query, visualize, and analyze Knowledge Assembly Models (KAMs) using Cytoscape.

The Plugin uses the BEL Framework Web Services application to access KAMs and create native Cytoscape networks that can be analyzed and manipulated using the rich set of network-centric Cytoscape tools.

The KAM Navigator plugin was developed with two main goals:

  • To illustrate how the BEL Framework can easily interoperate with existing technologies, especially those which have a large community around them, and
  • To illustrate how to use the BEL Framework Web Services API to create innovative and interesting knowledge-aware applications.

The KAM Navigator plugin was designed and developed by Selventa and is being released to the public. As part of this project, the source code for the KAM Navigator plugin is being made available.

Requirements

KAM Navigator is compatible with Cytoscape version 2.8 and the BEL Framework 2.0.0 or later.

Quick Start

  1. Download and install Cytoscape.

  2. Start Cytoscape and select Plugins -> Manage Plugins from the main menu. The plugin manager window will be displayed.

  3. Install the plugin by using the following URL in the Cytoscape Plugin Manager:

    https://raw.github.com/OpenBEL/Cytoscape-Plugins/master/plugins.xml

  1. Connect the plugin to the public demo server by setting the Webservice Location (WSDL URL) to:

    http://demo.openbel.org/openbel-ws/belframework.wsdl

  2. Load up one of our example KAMs.

To use the KAM Navigator plugin with your own KAMs you must have the OpenBEL Framework Web Services application running. See the OpenBEL website for more information on compiling KAMs and starting the OpenBEL Framework Web Services application.

Latest Release

0.9

  • Updated to OpenBEL 2.0.0, the newly open sourced framework
  • Networks with KAM attached elements can now be saved and reloaded and will properly reattach to the KAM they were loaded from, assuming the KAM is still present
  • Remove separate step for KAM load, now KAMs are loaded as you search for nodes
  • Misc bugfixes and improvements

Refer to the full Changelog for the changes in previous releases.

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